[Bioperl-l] parsing BLASTX

Brian Osborne brian_osborne at cognia.com
Thu May 20 07:54:37 EDT 2004


Yes, you should write your own script. Bioperl is really more of a “toolbox”
for writing scripts than a collection of scripts, although you can check out
the available scripts at http://bioperl.org/Core/Latest/bioscripts.html
(“bioscripts.pod”). Use that first script in the HOWTO - all you need to do
is add a “#!/bin/perl” line at the top of your script, use the correct name
for your BLASTX file instead of “report.bls”, and you should have a working
script. You must have Perl and Bioperl installed, forgive me for stating the

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Javier Terol
Sent: Tuesday, May 18, 2004 6:00 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] parsing BLASTX


I am an absolute begginer in the use of perl and bioperl modules. I am
interested in parsing a flile resulted from BLASTX. I have installed the
Bio:SearchIO modules, but after reading the HOWTO I did no get a clear idea
about what to do. Am I supossed to write my own scripts? How can I run the
SearchIO modules?
I would appreciate very much a step by step "protocol" for parsing the
blastx file, from the begining.

Thank you very much in advance.


  @@@O@@O@      Javier Terol Alcayde
  @O@@@@O@      Instituto Valenciano de Investigaciones Agrarias (IVIA)
  @@@O@@@@      Carretera Moncada - Náquera, Km. 4,5
   @@@@O@       46113 Moncada (Valencia)
     ||         Tel.     96 342 4000 ext. 70160
     ||         Fax.    96 342 4001

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